Week 7:

Hi guys! I'm so sorry for the late post! Hope you guys have been enjoying your internships and has a great spring break. It's already past week 7!

Well anyways, here's what I've been up to. Even though it was Spring Break last week, I still had to go to my internship. On Monday, we finally received the new primers that Dario and I designed the week before. I diluted the new primers and prepared the forward and reverse primer mixes. Then, I prepared for a PCR on the new primers with just the O. glaberrima parent (we ran out of O.barthii and the heterozygous parents).

On Wednesday, I ran a gel of the PCR reaction from Monday. Unfortunately, most of the primer combinations did not work, and most of them were the sh4 primers which are linked to the sh4 gene related to shattering. This gene is said to be involved in the development of the abscission layer which is a layer of cells that disintegrates leading the grains to fall off, or shatter. Of the 5 out of 15 primer combinations that did work, we prepared a new PCR with a new condition where we did a 40 second extension step instead of a minute and 20 seconds at 72 degrees Celsius.

I also finished reading the article from last week. Basically, the article talks about the good traits of O. glaberrima such as weed competitiveness, drought resistance, and tolerance for abiotic stresses such as acidic conditions and iron and aluminum toxicity. If combined with O.sativa and its high-yielding traits then we can produce a new kind of rice called NERICA (NEw RIce for AfriCA). However, there some interspecific incompatibility such as sterilization. There are still many questions on this that are unanswered.

Finally, on Friday, I did a PCR and a gel on a DNA plate with the down1 primer which is downstream from the focus target of the gene. Also, I had to make a nice (meaning really pretty and clear) gel of the 5 primer combinations that amplified earlier that week. Sadly, most of the bands were hard to distinguish since the O. glaberrima and the O. barthii parents were so close together. Even the known-heterozygous parent (which is just a mixture of glaberrima and barthii) had only one band when there should be two. After looking at the results, Dario and I concluded that we'll just have to design more new primers later.

Also, the PacBio (Pacific Biosciences) came in last week. They set up and performed some test runs. It seems like they're going to start using it this week.

Well, here's my Week 7! Sorry for the late post. I'll post up my Week 8 at the end of this week. Until then...See ya! Hope you guys have another great week!